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path: root/gn2/wqflask/views.py
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2024-07-30Fix GN3 URIs for case attribute editingzsloan
Also improve error logging somewhat (but still need to properly display the error in a template)
2024-07-03Add link to GeneCup to tool buttonszsloan
This also includes a function for converting a list of traits/datasets to symbols, which was added to trait.py
2024-05-29Handle attributeError when getting error codes.Alexander_Kabui
2024-05-28BugFix: return correct status code for generic exceptions handler.Alexander_Kabui
2024-05-20Check metadata exists before setting 'editable' field in get_dataset.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-13Disable gnqa functionality.Alexander_Kabui
* to test the functionality use ga.genenetwork.org
2024-05-09Remove debug statements.Alexander_Kabui
2024-05-09Improve error messaging for errors in gn fahamu UI.Alexander_Kabui
2024-04-30Use a dataset's label instead of it's id when fetching auth details.Munyoki Kilyungi
* gn2/wqflask/views.py (get_dataset): Use a dataset's label as it's identifier. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-23Create an endpoint for gnqa test templateAlexander_Kabui
2024-04-11Merge pull request #838 from genenetwork/feature/refactor-gnqa-uiAlexander Kabui
Feature/refactor gnqa UI
2024-04-05Refactor gnqa history endpoint.Alexander_Kabui
* require gn-auth
2024-04-05Update gnqa rating route.Alexander_Kabui
2024-04-02Use the dataset id to fetch the authorisation roles.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-27Require ouath2 for gnqa history search.Munyoki Kilyungi
* gn2/wqflask/views.py (gnqna_hist): Add "require_oauth2" decorator. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Co-authored-by: Alexander Kabui <alexanderkabua@gmail.com>
2024-03-27Require log-in to use the gn-qa search system.Munyoki Kilyungi
* gn2/wqflask/views.py: Import require_oauth2. (gnqna): Add "require_oauth2" decorator. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Co-authored-by: Alexander Kabui <alexanderkabua@gmail.com>
2024-03-26Only display the "edit" link when a user has edit permissions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Import user_logged_in from the clients module.Munyoki Kilyungi
Importing "user_logged_in" in the checks module just to export adds a layer of indirection and makes the code hard to read. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Remove unused imports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Remove unused declared variable.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Delete search dataset functionality in RDF.Munyoki Kilyungi
* gn2/wqflask/views.py (search_for_dataset): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26Delete unused page.Munyoki Kilyungi
* gn2/wqflask/views.py (display_diffs_admin): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-22add gnqa evaluation UIAlexander_Kabui
2024-03-05disable login requirement for gnqa on cdAlexander_Kabui
* reason gnqa and gn-auth are currently unstable
2024-02-16pep8 formattingAlexander_Kabui
2024-02-16init check for user loginAlexander_Kabui
2024-01-25add view point for gnqa search historyAlexander_Kabui
2024-01-16add UI for reference rating gn-llm documentsAlexander_Kabui
2024-01-12Switch NCBI link from http to https in failing test and RDF query.Munyoki Kilyungi
* gn2/tests/wqflask/show_trait/test_show_trait.py (test_get_ncbi_summary_request): Replace "http://eutils.ncbi.nlm.nih.gov" with "https://eutils.ncbi.nlm.nih.gov" * gn2/wqflask/views.py (get_probeset): Ditto. Co-authored-by: Alexander Kabui <Alexanderkabua@gmail.com> Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-10Add dataset metadata to genotype page when a dataset is specified.Munyoki Kilyungi
* gn2/wqflask/templates/genotype.html: Add extra dataset metadata. * gn2/wqflask/views.py (get_genotype): Extend genotype URL to enable specifying the dataset name. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-09Update script's module path.Frederick Muriuki Muriithi
2024-01-08Include Entrez summary for a geneID on the ProbeSet page.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-08Add dataset metadata to probeset page when a dataset is specified.Munyoki Kilyungi
* gn2/wqflask/templates/probeset.html: Add extra dataset metadata elements for groups, species, tissue name and dataset link. * gn2/wqflask/views.py (get_probeset): Extend probeset URL to enable specifying the dataset name. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-08revert to use GN3_LOCAL_URL for gn3 api endpointAlexander_Kabui
2024-01-08fix url errorAlexander_Kabui
2024-01-08fix url errorAlexander_Kabui
2024-01-08merge testingAlexander_Kabui
2024-01-08revert commit gn server urlAlexander_Kabui
2024-01-06Add probeset RDF page.Munyoki Kilyungi
* gn2/wqflask/templates/probeset.html: New probeset HTML file. * gn2/wqflask/views.py (get_probeset): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-05fix errorAlexander_Kabui
2024-01-05fetch gn_server_url from current configAlexander_Kabui
2024-01-02Fix path to error GIFs.Arun Isaac
genenetwork2 is now run from the top-level directory of the repo. So, we prepend gn2 to the error GIF path. * gn2/wqflask/views.py (handle_generic_exceptions): Prepend gn2 to error GIF path.
2024-01-02Change the way the info button works so that it just submits a form instead ↵zsloan
of opening a window with JS
2024-01-02Consistently use GN_VERSION from app config.Arun Isaac
GN_VERSION is set in the configuration file and read into the app config dictionary. Use that instead of re-reading from the etc/VERSION file. * gn2/utility/tools.py (gn_version): Delete function. (GN_VERSION): Delete variable. * gn2/wqflask/metadata_edits.py (display_phenotype_metadata, display_probeset_metadata, show_history): Use GN_VERSION in app config. * gn2/wqflask/views.py: Do not import GN_VERSION from gn2.utility.tools. (handle_generic_exceptions, index_page.__render__, submit_trait_form): Use GN_VERSION in app config.
2023-12-29Namespace all modules under gn2.Arun Isaac
We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service.
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